Summary

Summary {data-width=650}

Manhattan plot

manhattan_plot

manhattan_plot

QQ plot

qq_plot

qq_plot

AF plot

af_plot

af_plot

P-Z plot

pz_plot

pz_plot

beta_std plot

beta_std_plot

beta_std_plot

Metadata

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LDSC

*********************************************************************
* LD Score Regression (LDSC)
* Version 1.0.1
* (C) 2014-2019 Brendan Bulik-Sullivan and Hilary Finucane
* Broad Institute of MIT and Harvard / MIT Department of Mathematics
* GNU General Public License v3
*********************************************************************
Call: 
./ldsc.py \
--h2 /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1111/ieu-a-1111.vcf.gz \
--ref-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ \
--out /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1111/ldsc.txt \
--w-ld-chr /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/ 

Beginning analysis at Wed Feb  5 10:40:06 2020
Reading summary statistics from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/ieu-a-import/processed/ieu-a-1111/ieu-a-1111.vcf.gz ...
Read summary statistics for 2410957 SNPs.
Reading reference panel LD Score from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/[1-22] ...
Read reference panel LD Scores for 1290028 SNPs.
Removing partitioned LD Scores with zero variance.
Reading regression weight LD Score from /mnt/storage/private/mrcieu/research/scratch/IGD/data/dev/reference/eur_w_ld_chr/[1-22] ...
Read regression weight LD Scores for 1290028 SNPs.
After merging with reference panel LD, 1149510 SNPs remain.
After merging with regression SNP LD, 1149510 SNPs remain.
Using two-step estimator with cutoff at 30.
Total Observed scale h2: -0.0109 (0.0223)
Lambda GC: 1.0119
Mean Chi^2: 1.0186
Intercept: 1.0231 (0.0066)
Ratio: 1.2384 (0.3532)
Analysis finished at Wed Feb  5 10:40:33 2020
Total time elapsed: 27.53s

QC metrics

Metrics

Metrics

{
    "af_correlation": 0.9225,
    "inflation_factor": 1.0141,
    "mean_EFFECT": 0.0044,
    "n": 20675,
    "n_snps": 2410957,
    "n_clumped_hits": 0,
    "n_p_sig": 0,
    "n_mono": 0,
    "n_ns": 0,
    "n_mac": 0,
    "is_snpid_unique": true,
    "n_miss_EFFECT": 0,
    "n_miss_SE": 0,
    "n_miss_PVAL": 0,
    "n_miss_AF": 0,
    "n_miss_AF_reference": 19754,
    "n_est": 20251.5636,
    "ratio_se_n": 0.9897,
    "mean_diff": -0.0033,
    "ratio_diff": 86.1636,
    "sd_y_est1": 3.7444,
    "sd_y_est2": 3.7058,
    "r2_sum1": 0,
    "r2_sum2": 0,
    "r2_sum3": 0,
    "r2_sum4": 0,
    "ldsc_nsnp_merge_refpanel_ld": 1149510,
    "ldsc_nsnp_merge_regression_ld": 1149510,
    "ldsc_observed_scale_h2_beta": "NA",
    "ldsc_observed_scale_h2_se": "NA",
    "ldsc_intercept_beta": 1.0231,
    "ldsc_intercept_se": 0.0066,
    "ldsc_lambda_gc": 1.0119,
    "ldsc_mean_chisq": 1.0186,
    "ldsc_ratio": 1.2419
}

Flags

name value
af_correlation FALSE
inflation_factor FALSE
n FALSE
is_snpid_non_unique FALSE
mean_EFFECT_nonfinite FALSE
mean_EFFECT_05 FALSE
mean_EFFECT_01 FALSE
mean_chisq FALSE
n_p_sig FALSE
miss_EFFECT FALSE
miss_SE FALSE
miss_PVAL FALSE
ldsc_ratio TRUE
ldsc_intercept_beta FALSE
n_clumped_hits FALSE
r2_sum1 FALSE
r2_sum2 FALSE
r2_sum3 FALSE
r2_sum4 FALSE

Definitions

General metrics

  • af_correlation: Correlation coefficient between AF and AF_reference.
  • inflation_factor (lambda): Genomic inflation factor.
  • mean_EFFECT: Mean of EFFECT size.
  • n: Maximum value of reported sample size across all SNPs, \(n\).
  • n_clumped_hits: Number of clumped hits.
  • n_snps: Number of SNPs
  • n_p_sig: Number of SNPs with pvalue below 5e-8.
  • n_mono: Number of monomorphic (MAF == 1 or MAF == 0) SNPs.
  • n_ns: Number of SNPs with nonsense values:
    • alleles other than A, C, G or T.
    • P-values < 0 or > 1.
    • negative or infinite standard errors (<= 0 or = Infinity).
    • infinite beta estimates or allele frequencies < 0 or > 1.
  • n_mac: Number of cases where MAC (\(2 \times N \times MAF\)) is less than 6.
  • is_snpid_unique: true if the combination of ID REF ALT is unique and therefore no duplication in snpid.
  • n_miss_<*>: Number of NA observations for <*> column.

se_n metrics

  • n_est: Estimated sample size value, \(\widehat{n}\).
  • ratio_se_n: \(\texttt{ratio_se_n} = \frac{\sqrt{\widehat{n}}}{\sqrt{n}}\). We expect ratio_se_n to be 1. When it is not 1, it implies that the trait did not have a variance of 1, the reported sample size is wrong, or that the SNP-level effective sample sizes differ markedly from the reported sample size.
  • mean_diff: \(\texttt{mean_diff} = \sum_{j} \frac{\widehat{\beta_j^{std}} - \beta_j}{\texttt{n_snps}}\), mean difference between the standardised beta, predicted from P-values, and the observed beta. The difference should be very close to zero if trait has a variance of 1.
    • \(\widehat{\beta_j^{std}} = \sqrt{\frac{{z}_j^2 / ({z}_j^2 + n -2)}{2 \times {MAF}_j \times (1 - {MAF}_j)}} \times sign({z}_j)\),
    • \({z}_j = \frac{\beta_j}{{se}_j}\),
    • and \(\beta_j\) is the reported effect size.
  • ratio_diff: \(\texttt{ratio_diff} = |\frac{\texttt{mean_diff}}{\texttt{mean_diff2}}|\), absolute ratio between the mean of diff and the mean of diff2 (expected difference between the standardised beta predicted from P-values, and the standardised beta derived from the observed beta divided by the predicted SD; NOT reported). The ratio should be close to 1. If different from 1, then implies that the betas are not in a standard deviation scale.
    • \(\texttt{mean_diff2} = \sum_{j} \frac{\widehat{\beta_j^{std}} - \beta^{\prime}_j}{\texttt{n_snps}}\)
    • \(\beta^{\prime}_j = \frac{\beta_j}{\widehat{\texttt{sd2}}_{y}}\)
  • sd_y_est1: The standard deviation for the trait inferred from the reported sample size, median standard errors for the SNP-trait assocations and SNP variances.
    • \(\widehat{\texttt{sd1}}_{y} = \frac{\sqrt{n} \times median({se}_j)}{C}\),
    • \(C = median(\frac{1}{\sqrt{2 \times {MAF}_j \times (1 - {MAF}_j)}})\),
    • and \({se}_j\) is the reported standard error.
  • sd_y_est2: The standard deviation for the trait inferred from the reported sample size, Z statistics for the SNP-trait effects (beta/se) and allele frequency.
    • \(\widehat{\texttt{sd2}}_{y} = median(\widehat{sd_j})\),
    • \(\widehat{sd_j} = \frac{\beta_j}{\widehat{\beta_j^{std}}}\),

r2 metrics

Sum of variance explained, calculated from the clumped top hits sample.

  • r2_sum<*>: r2 statistics under various assumptions
    • 1: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var1}}}\), \(\texttt{var1} = 1\).
    • 2: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var2}}}\), \(\texttt{var2} = {\widehat{\texttt{sd1}}_{y}}^2\),
    • 3: \(r^2 = \sum_j{\frac{2 \times \beta_j^2 \times {MAF}_j \times (1 - {MAF}_j)}{\texttt{var3}}}\), \(\texttt{var3} = {\widehat{\texttt{sd2}}_{y}}^2\),
    • 4: \(r^2 = \sum_j{\frac{F_j}{F_j + n - 2}}\), \(F = \frac{\beta_j^2}{{se}_j^2}\).

LDSC metrics

Metrics from LD regression

  • ldsc_nsnp_merge_refpanel_ld: Number of remaining SNPs after merging with reference panel LD.
  • ldsc_nsnp_merge_regression_ld: Number of remaining SNPs after merging with regression SNP LD.
  • ldsc_observed_scale_h2_{beta,se} Coefficient value and SE for total observed scale h2.
  • ldsc_intercept_{beta,se}: Coefficient value and SE for intercept. Intercept is expected to be 1.
  • ldsc_lambda_gc: Lambda GC statistics.
  • ldsc_mean_chisq: Mean \(\chi^2\) statistics.
  • ldsc_ratio: \(\frac{\texttt{ldsc_intercept_beta} - 1}{\texttt{ldsc_mean_chisq} - 1}\), the proportion of the inflation in the mean \(\chi^2\) that the LD Score regression intercepts ascribes to causes other than polygenic heritability. The value of ratio should be close to zero, though in practice values of 0.1-0.2 are not uncommon, probably due to sample/reference LD Score mismatch or model misspecification (e.g., low LD variants have slightly higher \(h^2\) per SNP).

Flags

When a metric needs attention, the flag should return TRUE.

  • af_correlation: abs(af_correlation) < 0.7.
  • inflation_factor: inflation_factor > 1.2.
  • n: n (max reported sample size) < 10000.
  • is_snpid_non_unique: NOT is_snpid_unique.
  • mean_EFFECT_nonfinite: mean(EFFECT) is NA, NaN, or Inf.
  • mean_EFFECT_05: abs(mean(EFFECT)) > 0.5.
  • mean_EFFECT_01: abs(mean(EFFECT)) > 0.1.
  • mean_chisq: ldsc_mean_chisq > 1.3 or ldsc_mean_chisq < 0.7.
  • n_p_sig: n_p_sig > 1000.
  • miss_<*>: n_miss_<*> / n_snps > 0.01.
  • ldsc_ratio: ldsc_ratio > 0.5
  • ldsc_intercept_beta: ldsc_intercept_beta > 1.5
  • n_clumped_hits: n_clumped_hits > 1000
  • r2_sum<*>: r2_sum<*> > 0.5

Plots

  • Manhattan plot
    • Red line: \(-log_{10}^{5 \times 10^{-8}}\)
    • Blue line: \(-log_{10}^{5 \times 10^{-5}}\)
  • QQ plot
  • AF plot
  • P-Z plot
  • beta_std plot: Scatter plot between \(\widehat{\beta_j^{std}}\) and \(\beta_j\)

Diagnostics

Details

Summary stats

skim_type skim_variable n_missing complete_rate character.min character.max character.empty character.n_unique character.whitespace numeric.mean numeric.sd numeric.p0 numeric.p25 numeric.p50 numeric.p75 numeric.p100 numeric.hist
character ID 0 1.0000000 3 42 0 2410957 0 NA NA NA NA NA NA NA NA
character REF 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
character ALT 0 1.0000000 1 1 0 4 0 NA NA NA NA NA NA NA NA
numeric CHROM 0 1.0000000 NA NA NA NA NA 8.597084e+00 5.660337e+00 1.0000e+00 4.000000e+00 8.000000e+00 1.200000e+01 2.30000e+01 ▇▅▅▂▂
numeric POS 0 1.0000000 NA NA NA NA NA 7.877812e+07 5.565977e+07 1.1523e+04 3.259685e+07 7.017937e+07 1.142890e+08 2.49219e+08 ▇▆▅▂▁
numeric EFFECT 0 1.0000000 NA NA NA NA NA 4.428300e-03 6.341710e-02 -1.0956e+00 -3.000000e-02 2.700000e-03 3.650000e-02 1.15120e+00 ▁▁▇▁▁
numeric SE 0 1.0000000 NA NA NA NA NA 5.571550e-02 2.931640e-02 3.4200e-02 3.810000e-02 4.430000e-02 6.010000e-02 4.83900e-01 ▇▁▁▁▁
numeric PVAL 0 1.0000000 NA NA NA NA NA 4.972761e-01 2.897939e-01 1.0000e-07 2.450000e-01 4.969996e-01 7.486003e-01 1.00000e+00 ▇▇▇▇▇
numeric PVAL_ztest 0 1.0000000 NA NA NA NA NA 4.972759e-01 2.897943e-01 1.0000e-07 2.450013e-01 4.970384e-01 7.485796e-01 1.00000e+00 ▇▇▇▇▇
numeric AF 0 1.0000000 NA NA NA NA NA 3.642258e-01 2.654131e-01 1.0500e-02 1.342000e-01 2.999000e-01 5.595000e-01 9.89200e-01 ▇▅▃▃▂
numeric AF_reference 19754 0.9918066 NA NA NA NA NA 3.647549e-01 2.538362e-01 1.9970e-04 1.513580e-01 3.043130e-01 5.483230e-01 1.00000e+00 ▇▆▅▃▂
numeric N 0 1.0000000 NA NA NA NA NA 2.067500e+04 0.000000e+00 2.0675e+04 2.067500e+04 2.067500e+04 2.067500e+04 2.06750e+04 ▁▁▇▁▁

Head and tail

CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
1 752566 rs3094315 G A 0.0377 0.0816 0.6438000 0.6440743 0.8368 0.718251 20675
1 768448 rs12562034 G A -0.0468 0.0759 0.5375997 0.5374981 0.1000 0.191893 20675
1 785989 rs2980300 T C -0.0863 0.1106 0.4354998 0.4352206 0.8690 0.626997 20675
1 990380 rs3121561 C T 0.0240 0.0609 0.6939002 0.6935156 0.2778 0.343450 20675
1 998501 rs3813193 G C -0.0472 0.0583 0.4184003 0.4181670 0.1660 0.206669 20675
1 1003629 rs4075116 C T -0.0677 0.0482 0.1598001 0.1601509 0.7390 0.720647 20675
1 1005806 rs3934834 C T -0.0364 0.0522 0.4861004 0.4856038 0.1493 0.223442 20675
1 1017170 rs3766193 C G -0.0226 0.0401 0.5731998 0.5730325 0.5522 0.575479 20675
1 1017197 rs3766192 C T -0.0190 0.0376 0.6143997 0.6133347 0.5606 0.511182 20675
1 1017587 rs3766191 C T -0.0499 0.0552 0.3659999 0.3660031 0.1436 0.171126 20675
CHROM POS ID REF ALT EFFECT SE PVAL PVAL_ztest AF AF_reference N
22 51178090 rs2285395 G A 0.0085 0.0823 0.9179001 0.9177402 0.0841 0.0666933 20675
22 51196164 rs8136603 A T -0.0152 0.1118 0.8922000 0.8918552 0.0527 0.1427720 20675
22 51216564 rs9616970 T C -0.0282 0.1064 0.7909991 0.7909805 0.1627 0.1563500 20675
22 51222100 rs114553188 G T -0.1279 0.1261 0.3105997 0.3104518 0.0540 0.0880591 20675
22 51223637 rs375798137 G A -0.1276 0.1265 0.3132997 0.3131206 0.0540 0.0788738 20675
23 35921591 rs2204667 C G -0.0208 0.0545 0.7023005 0.7027200 0.1576 NA 20675
23 51666786 rs14115 A G 0.0581 0.0782 0.4577001 0.4575018 0.0503 NA 20675
23 70163799 rs1626496 A C 0.0493 0.0673 0.4640000 0.4638385 0.0822 NA 20675
23 91415872 rs6562597 G A -0.0080 0.1316 0.9517001 0.9515262 0.0231 0.0021192 20675
23 118495837 rs12882977 G A -0.0722 0.0394 0.0667606 0.0668789 0.4988 0.2307280 20675

bcf preview

1   752566  rs3094315   G   A   .   PASS    AF=0.8368   ES:SE:LP:AF:SS:ID   0.0377:0.0816:0.191249:0.8368:20675:rs3094315
1   768448  rs12562034  G   A   .   PASS    AF=0.1  ES:SE:LP:AF:SS:ID   -0.0468:0.0759:0.269541:0.1:20675:rs12562034
1   785989  rs2980300   T   C   .   PASS    AF=0.869    ES:SE:LP:AF:SS:ID   -0.0863:0.1106:0.361012:0.869:20675:rs2980300
1   990380  rs3121561   C   T   .   PASS    AF=0.2778   ES:SE:LP:AF:SS:ID   0.024:0.0609:0.158703:0.2778:20675:rs3121561
1   998501  rs3813193   G   C   .   PASS    AF=0.166    ES:SE:LP:AF:SS:ID   -0.0472:0.0583:0.378408:0.166:20675:rs3813193
1   1003629 rs4075116   C   T   .   PASS    AF=0.739    ES:SE:LP:AF:SS:ID   -0.0677:0.0482:0.796423:0.739:20675:rs4075116
1   1005806 rs3934834   C   T   .   PASS    AF=0.1493   ES:SE:LP:AF:SS:ID   -0.0364:0.0522:0.313274:0.1493:20675:rs3934834
1   1017170 rs3766193   C   G   .   PASS    AF=0.5522   ES:SE:LP:AF:SS:ID   -0.0226:0.0401:0.241694:0.5522:20675:rs3766193
1   1017197 rs3766192   C   T   .   PASS    AF=0.5606   ES:SE:LP:AF:SS:ID   -0.019:0.0376:0.211549:0.5606:20675:rs3766192
1   1017587 rs3766191   C   T   .   PASS    AF=0.1436   ES:SE:LP:AF:SS:ID   -0.0499:0.0552:0.436519:0.1436:20675:rs3766191
1   1018562 rs9442371   C   T   .   PASS    AF=0.5701   ES:SE:LP:AF:SS:ID   -0.0075:0.0379:0.0742755:0.5701:20675:rs9442371
1   1018704 rs9442372   A   G   .   PASS    AF=0.5701   ES:SE:LP:AF:SS:ID   -0.019:0.0367:0.218532:0.5701:20675:rs9442372
1   1021346 rs10907177  A   G   .   PASS    AF=0.1447   ES:SE:LP:AF:SS:ID   -0.0623:0.056:0.575608:0.1447:20675:rs10907177
1   1021415 rs3737728   A   G   .   PASS    AF=0.7204   ES:SE:LP:AF:SS:ID   -0.0522:0.04:0.716473:0.7204:20675:rs3737728
1   1021583 rs10907178  A   C   .   PASS    AF=0.143    ES:SE:LP:AF:SS:ID   -0.0653:0.0566:0.603801:0.143:20675:rs10907178
1   1021695 rs9442398   A   G   .   PASS    AF=0.7273   ES:SE:LP:AF:SS:ID   -0.0548:0.0425:0.703993:0.7273:20675:rs9442398
1   1022037 rs6701114   C   T   .   PASS    AF=0.5543   ES:SE:LP:AF:SS:ID   -0.0113:0.0404:0.10824:0.5543:20675:rs6701114
1   1026707 rs4074137   C   A   .   PASS    AF=0.5967   ES:SE:LP:AF:SS:ID   -0.0245:0.0405:0.263285:0.5967:20675:rs4074137
1   1030565 rs6687776   C   T   .   PASS    AF=0.1565   ES:SE:LP:AF:SS:ID   0.0546:0.0487:0.580871:0.1565:20675:rs6687776
1   1030633 rs6678318   G   A   .   PASS    AF=0.1563   ES:SE:LP:AF:SS:ID   0.0742:0.0497:0.86742:0.1563:20675:rs6678318
1   1031540 rs9651273   A   G   .   PASS    AF=0.7317   ES:SE:LP:AF:SS:ID   0.0251:0.0417:0.261537:0.7317:20675:rs9651273
1   1036959 rs11579015  T   C   .   PASS    AF=0.1127   ES:SE:LP:AF:SS:ID   0.1225:0.0581:1.45457:0.1127:20675:rs11579015
1   1040026 rs6671356   T   C   .   PASS    AF=0.1412   ES:SE:LP:AF:SS:ID   0.1268:0.0529:1.78252:0.1412:20675:rs6671356
1   1046164 rs6666280   C   T   .   PASS    AF=0.1348   ES:SE:LP:AF:SS:ID   0.1531:0.053:2.41229:0.1348:20675:rs6666280
1   1048955 rs4970405   A   G   .   PASS    AF=0.1057   ES:SE:LP:AF:SS:ID   0.1449:0.0578:1.91507:0.1057:20675:rs4970405
1   1049950 rs12726255  A   G   .   PASS    AF=0.1351   ES:SE:LP:AF:SS:ID   0.145:0.0518:2.29175:0.1351:20675:rs12726255
1   1053452 rs4970409   G   A   .   PASS    AF=0.1073   ES:SE:LP:AF:SS:ID   0.1397:0.0583:1.78068:0.1073:20675:rs4970409
1   1060174 rs7548798   C   T   .   PASS    AF=0.3154   ES:SE:LP:AF:SS:ID   0.0003:0.0447:0.00252624:0.3154:20675:rs7548798
1   1060235 rs7540009   G   A   .   PASS    AF=0.0294   ES:SE:LP:AF:SS:ID   0.1639:0.13:0.682982:0.0294:20675:rs7540009
1   1060608 rs17160824  G   A   .   PASS    AF=0.1172   ES:SE:LP:AF:SS:ID   0.1423:0.0587:1.81446:0.1172:20675:rs17160824
1   1061115 rs17160826  T   C   .   PASS    AF=0.1067   ES:SE:LP:AF:SS:ID   0.1418:0.0587:1.80272:0.1067:20675:rs17160826
1   1061152 rs12748370  T   C   .   PASS    AF=0.1066   ES:SE:LP:AF:SS:ID   0.1422:0.0588:1.80827:0.1066:20675:rs12748370
1   1061166 rs11807848  T   C   .   PASS    AF=0.4051   ES:SE:LP:AF:SS:ID   0.0518:0.0395:0.721246:0.4051:20675:rs11807848
1   1062015 rs9659914   C   T   .   PASS    AF=0.0288   ES:SE:LP:AF:SS:ID   0.1302:0.1402:0.452348:0.0288:20675:rs9659914
1   1062638 rs9442373   C   A   .   PASS    AF=0.5547   ES:SE:LP:AF:SS:ID   -0.0533:0.0382:0.786482:0.5547:20675:rs9442373
1   1064535 rs6682475   G   C   .   PASS    AF=0.7205   ES:SE:LP:AF:SS:ID   -0.1168:0.0544:1.4973:0.7205:20675:rs6682475
1   1064979 rs2298217   C   T   .   PASS    AF=0.1471   ES:SE:LP:AF:SS:ID   0.0829:0.0503:1.00423:0.1471:20675:rs2298217
1   1066029 rs12145826  G   A   .   PASS    AF=0.0716   ES:SE:LP:AF:SS:ID   -0.0058:0.085:0.0242007:0.0716:20675:rs12145826
1   1066403 rs10907182  T   C   .   PASS    AF=0.6267   ES:SE:LP:AF:SS:ID   -0.0649:0.0472:0.772113:0.6267:20675:rs10907182
1   1071118 rs10907183  G   C   .   PASS    AF=0.6438   ES:SE:LP:AF:SS:ID   -0.074:0.0501:0.853252:0.6438:20675:rs10907183
1   1077064 rs4970357   C   A   .   PASS    AF=0.9167   ES:SE:LP:AF:SS:ID   -0.0337:0.093:0.14442:0.9167:20675:rs4970357
1   1079198 rs11260603  T   C   .   PASS    AF=0.2304   ES:SE:LP:AF:SS:ID   0.0713:0.0595:0.636576:0.2304:20675:rs11260603
1   1087683 rs9442380   T   C   .   PASS    AF=0.9227   ES:SE:LP:AF:SS:ID   -0.0703:0.0718:0.483994:0.9227:20675:rs9442380
1   1089262 rs4970358   A   G   .   PASS    AF=0.9534   ES:SE:LP:AF:SS:ID   -0.0604:0.1105:0.233215:0.9534:20675:rs4970358
1   1094738 rs4970362   A   G   .   PASS    AF=0.6377   ES:SE:LP:AF:SS:ID   -0.0605:0.0425:0.810229:0.6377:20675:rs4970362
1   1097335 rs9442385   T   G   .   PASS    AF=0.9335   ES:SE:LP:AF:SS:ID   -0.076:0.0784:0.478078:0.9335:20675:rs9442385
1   1099342 rs9660710   A   C   .   PASS    AF=0.9336   ES:SE:LP:AF:SS:ID   -0.0735:0.0708:0.524184:0.9336:20675:rs9660710
1   1100217 rs1891905   C   T   .   PASS    AF=0.956    ES:SE:LP:AF:SS:ID   -0.1313:0.1164:0.585528:0.956:20675:rs1891905
1   1106473 rs4970420   G   A   .   PASS    AF=0.1749   ES:SE:LP:AF:SS:ID   -0.0931:0.0635:0.84588:0.1749:20675:rs4970420
1   1119858 rs1320565   C   T   .   PASS    AF=0.0774   ES:SE:LP:AF:SS:ID   -0.0328:0.0765:0.174834:0.0774:20675:rs1320565